Search Results - "Crabtree, Jonathan"

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium by Sinha, Rashmi, Abu-Ali, Galeb, Vogtmann, Emily, Fodor, Anthony A, Ren, Boyu, Amir, Amnon, Schwager, Emma, Crabtree, Jonathan, Ma, Siyuan, Abnet, Christian C, Knight, Rob, White, Owen, Huttenhower, Curtis

“…The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of…”
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Strains, functions and dynamics in the expanded Human Microbiome Project by Lloyd-Price, Jason, Mahurkar, Anup, Rahnavard, Gholamali, Crabtree, Jonathan, Orvis, Joshua, Hall, A. Brantley, Brady, Arthur, Creasy, Heather H., McCracken, Carrie, Giglio, Michelle G., McDonald, Daniel, Franzosa, Eric A., Knight, Rob, White, Owen, Huttenhower, Curtis

“…The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity,…”
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A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina by Ma, Bing, France, Michael T., Crabtree, Jonathan, Holm, Johanna B., Humphrys, Michael S., Brotman, Rebecca M., Ravel, Jacques

“…Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference…”
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The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates by RASKO, David A, ROSOVITZ, M. J, HENDERSON, Ian R, SPERANDIO, Vanessa, RAVEL, Jacques, MYERS, Garry S. A, MONGODIN, Emmanuel F, FRICKE, W. Florian, GAJER, Pawel, CRABTREE, Jonathan, SEBAIHIA, Mohammed, THOMSON, Nicholas R, CHAUDHURI, Roy

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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An integrated genomic and transcriptomic survey of mucormycosis-causing fungi by Chibucos, Marcus C., Soliman, Sameh, Gebremariam, Teclegiorgis, Lee, Hongkyu, Daugherty, Sean, Orvis, Joshua, Shetty, Amol C., Crabtree, Jonathan, Hazen, Tracy H., Etienne, Kizee A., Kumari, Priti, O’Connor, Timothy D., Rasko, David A., Filler, Scott G., Fraser, Claire M., Lockhart, Shawn R., Skory, Christopher D., Ibrahim, Ashraf S., Bruno, Vincent M.

“…Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three…”
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Mutagenesis of human genomes by endogenous mobile elements on a population scale by Chuang, Nelson T, Gardner, Eugene J, Terry, Diane M, Crabtree, Jonathan, Mahurkar, Anup A, Rivell, Guillermo L, Hong, Charles C, Perry, James A, Devine, Scott E

“…Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional…”
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Functional dynamics of the gut microbiome in elderly people during probiotic consumption by Eloe-Fadrosh, Emiley A, Brady, Arthur, Crabtree, Jonathan, Drabek, Elliott F, Ma, Bing, Mahurkar, Anup, Ravel, Jacques, Haverkamp, Miriam, Fiorino, Anne-Maria, Botelho, Christine, Andreyeva, Irina, Hibberd, Patricia L, Fraser, Claire M

“…A mechanistic understanding of the purported health benefits conferred by consumption of probiotic bacteria has been limited by our knowledge of the resident…”
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Sub-telomere directed gene expression during initiation of invasive aspergillosis by McDonagh, Andrew, Fedorova, Natalie D, Crabtree, Jonathan, Yu, Yan, Kim, Stanley, Chen, Dan, Loss, Omar, Cairns, Timothy, Goldman, Gustavo, Armstrong-James, Darius, Haynes, Ken, Haas, Hubertus, Schrettl, Markus, May, Gregory, Nierman, William C, Bignell, Elaine

“…Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled…”
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Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic by Eppinger, Mark, Pearson, Talima, Koenig, Sara S K, Pearson, Ofori, Hicks, Nathan, Agrawal, Sonia, Sanjar, Fatemeh, Galens, Kevin, Daugherty, Sean, Crabtree, Jonathan, Hendriksen, Rene S, Price, Lance B, Upadhyay, Bishnu P, Shakya, Geeta, Fraser, Claire M, Ravel, Jacques, Keim, Paul S

“…For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a…”
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The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community by Arnaud, Martha B, Chibucos, Marcus C, Costanzo, Maria C, Crabtree, Jonathan, Inglis, Diane O, Lotia, Adil, Orvis, Joshua, Shah, Prachi, Skrzypek, Marek S, Binkley, Gail, Miyasato, Stuart R, Wortman, Jennifer R, Sherlock, Gavin

“…The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD…”
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Ergatis: a web interface and scalable software system for bioinformatics workflows by Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, Angiuoli, Samuel V.

“…Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems…”
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Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity by Palmateer, Nicholas C, Tretina, Kyle, Orvis, Joshua, Ifeonu, Olukemi O, Crabtree, Jonathan, Drabék, Elliott, Pelle, Roger, Awino, Elias, Gotia, Hanzel T, Munro, James B, Tallon, Luke, Morrison, W Ivan, Daubenberger, Claudia A, Nene, Vish, Knowles, Donald P, Bishop, Richard P, Silva, Joana C

“…Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against…”
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CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline by Agrawal, Sonia, Arze, Cesar, Adkins, Ricky S, Crabtree, Jonathan, Riley, David, Vangala, Mahesh, Galens, Kevin, Fraser, Claire M, Tettelin, Hervé, White, Owen, Angiuoli, Samuel V, Mahurkar, Anup, Fricke, W Florian

“…The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines…”
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Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz [version 2; peer review: 3 approved] by Wagner, Justin, Kancherla, Jayaram, Braccia, Domenick, Matsumara, James, Felix, Victor, Crabtree, Jonathan, Mahurkar, Anup, Corrada Bravo, Héctor

“…The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between…”
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New resources for functional analysis of omics data for the genus Aspergillus by Nitsche, Benjamin M, Crabtree, Jonathan, Cerqueira, Gustavo C, Meyer, Vera, Ram, Arthur F J, Wortman, Jennifer R

“…Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data. As such, Gene Ontology…”
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Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz [version 1; peer review: 3 approved] by Wagner, Justin, Kancherla, Jayaram, Braccia, Domenick, Matsumara, James, Felix, Victor, Crabtree, Jonathan, Mahurkar, Anup, Corrada Bravo, Héctor

“…The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between…”
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IDEA: Interactive Display for Evolutionary Analyses by Simons, Rain, Mahurkar, Anup, Crabtree, Jonathan, Badger, Jonathan H, Carlton, Jane M, Silva, Joana C

“…The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective…”
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Building on the Work of Colleagues: A Moment of Reflection by Jonathan D. Crabtree

“…Building on the Work of Colleagues: A Moment of Reflection…”
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HuRef Browser: a web resource for individual human genomics by Axelrod, Nelson, Lin, Yuan, Ng, Pauline C, Stockwell, Timothy B, Crabtree, Jonathan, Huang, Jiaqi, Kirkness, Ewen, Strausberg, Robert L, Frazier, Marvin E, Venter, J. Craig, Kravitz, Saul, Levy, Samuel

“…The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The…”
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Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps by Desjardins, Christopher A, Gundersen-Rindal, Dawn E, Hostetler, Jessica B, Tallon, Luke J, Fadrosh, Douglas W, Fuester, Roger W, Pedroni, Monica J, Haas, Brian J, Schatz, Michael C, Jones, Kristine M, Crabtree, Jonathan, Forberger, Heather, Nene, Vishvanath

“…Background: Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are…”
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